chr17-4810929-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_002663.5(PLD2):c.988C>T(p.Arg330Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,459,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R330Q) has been classified as Benign.
Frequency
Consequence
NM_002663.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLD2 | NM_002663.5 | c.988C>T | p.Arg330Trp | missense_variant | 10/25 | ENST00000263088.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLD2 | ENST00000263088.11 | c.988C>T | p.Arg330Trp | missense_variant | 10/25 | 1 | NM_002663.5 | P1 | |
PLD2 | ENST00000572940.5 | c.988C>T | p.Arg330Trp | missense_variant | 10/25 | 1 | |||
PLD2 | ENST00000575813.5 | c.124C>T | p.Arg42Trp | missense_variant, NMD_transcript_variant | 1/4 | 4 | |||
PLD2 | ENST00000575246.6 | c.*636C>T | 3_prime_UTR_variant, NMD_transcript_variant | 10/18 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248888Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134574
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459926Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726268
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 19, 2021 | The c.988C>T (p.R330W) alteration is located in exon 10 (coding exon 9) of the PLD2 gene. This alteration results from a C to T substitution at nucleotide position 988, causing the arginine (R) at amino acid position 330 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at